EP2726628A1 - Procédés de détection de fusions de gènes - Google Patents

Procédés de détection de fusions de gènes

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Publication number
EP2726628A1
EP2726628A1 EP11868918.1A EP11868918A EP2726628A1 EP 2726628 A1 EP2726628 A1 EP 2726628A1 EP 11868918 A EP11868918 A EP 11868918A EP 2726628 A1 EP2726628 A1 EP 2726628A1
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European Patent Office
Prior art keywords
probe
fusion
nucleic acid
sample
gene
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EP11868918.1A
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German (de)
English (en)
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EP2726628B1 (fr
EP2726628A4 (fr
Inventor
Bruce Seligmann
Bj Kerns
John Luecke
Matt ROUNSEVILLE
Ihab Botros
Mark Schwartz
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HTG Molecular Diagnostics Inc
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HTG Molecular Diagnostics Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • This disclosure relates to methods of detecting gene fusions, particularly oncogenic gene fusions.
  • a fusion gene is one type of mutation which is a hybrid gene formed from two previously separate genes or from previously non-contiguous regions of the same gene. It can occur, for example, as the result of a translocation, interstitial deletion, or chromosomal inversion.
  • tyrosine kinase genes which encode important enzymes directly regulating cell growth, have been reported to contain oncogenic mutations. Kinase activity can be activated, for example, by substitution or deletion in amino acid sequences and thereby bring about carcinogenesis or contribute to aggressive versus less aggressive cancers, or lead to a propensity for metastasis, or cause drug sensitivity or drug resistance.
  • the BCR-ABL gene fusion is one that has long been associated with cancer; in particular, chronic myelogenous leukemia (CML) and in some cases acute myelogenous leukemia (AML) or acute lymphoblastic leukemia (ALL).
  • CML4/ALK e.g., lung cancer
  • TMPRSS2/ERG e.g., prostate cancer
  • IgH/MYC e.g., Burkitt lymphoma
  • MYB/NFIB e.g., carcinomas of the breast and head and neck
  • TMPRSS2/ETV4 e.g., prostate cancer
  • EWSRl/FLIl e.g., Ewing sarcoma
  • neoplastic transformation it is known that some genes are highly promiscuous in that they may recombine with many different partners, for example, within the same tumor entities, e.g., MLL in acute leukemias (Collins and Rabbitts, Trends in Molecular Medicine, 8(9): 436-442 2002), EWSR1 in bone and soft tissue tumors (Helman and Meltzer, Nature Reviews Cancer, 3(9): 685-694, 2003), and RET in thyroid carcinomas (Pierotti, Nature Reviews Cancer, 1(3): 245- 250, 2001).
  • MLL in acute leukemias
  • EWSR1 in bone and soft tissue tumors
  • RET RET in thyroid carcinomas
  • ETV6-NTRK3 has been described in cancers as diverse as acute myeloid leukemia, infantile fibrosarcoma, mesoblastic nephroma, and breast carcinoma (Tognon et ah, Cancer Cell, 2(5): 367- 376, 2002). There are also several examples where seemingly identical
  • chromosomal aberrations produce different fusion genes.
  • One of the most common translocations in pre-B acute lymphoblastic leukemia, t(l;19)(q23;pl3) leading to a TCF3/PBX1 fusion, may result in a chimeric transcript consisting of two entirely different genes, MEF2D in lq23 and DAZAP1 in 19ql3 (Yuki et al, Cancer Science, 95 (6):503-507, 2004).
  • Gene fusions can be diagnostic markers or therapeutic targets, as well as useful for predicting patient prognosis and/or response to drugs. Further, it is clear that multiple fusions may arise in the same tumor or subject and/or that each subject may have medically relevant gene fusions that differ from other afflicted subjects. Accordingly, new technologies for detecting gene fusions are critically important to advance science and medicine.
  • the disclosed methods can be used to detect known gene fusions (such as a known gene translocation, interstitial deletion, or inversion) and in some examples, can also be used to detect previously unknown gene fusions, for example a fusion between two genes at a previously unidentified fusion point, or a fusion between two genes previously unknown to participate in a gene fusion.
  • the methods are highly sensitive and specific, optionally can be used to quantify detected gene fusions, and can be used to detect a gene fusion in any nucleic acid molecule, such as DNA or RNA.
  • the disclosed methods are also amenable to multiplexing, so as to detect multiple gene fusions in a sample from a subject, or to detect the same set of gene fusions (or set of genes, including some gene fusions) in samples from multiple subjects..
  • FIG. 1 is a schematic diagram showing exemplary wild-type genes (Genes 1 and 2) and a fusion gene and an exemplary fusion probe.
  • the fusion probe hybridizes and is detected following nuclease treatment (solid line).
  • the fusion probe only partially hybridizes to Genes 1 and 2 and at least the non-hybridized portion is hydrolyzed by the nuclease treatment (dotted lines).
  • FIG. 2 is a schematic diagram showing exemplary wild-type genes (Genes 1 and 2) and a fusion gene and an exemplary direct-labeled fusion probe having a four nucleotide overlap with the 5' portion of the fusion gene.
  • the label biotin in this example
  • the fusion probe hybridizes and the label is detected following nuclease treatment (top panel).
  • the fusion probe does not hybridize to Gene 1 and is hydrolyzed by the nuclease treatment (middle panel).
  • the fusion probe hybridizes to Gene 2; however the 5' end including the label does not hybridize and is cleaved by the nuclease treatment (bottom panel). Therefore, the labeled probe is only detected in samples where the gene fusion is present.
  • FIG. 3 is a schematic diagram showing exemplary full-length wild type genes (Genes 1 and 2) and a fusion gene and exemplary flanking probes and an exemplary fusion probe.
  • the fusion gene includes a 5' portion of Gene 1 and a 3' portion of Gene 2.
  • the flanking 5' probe 1 and 3' probe 1 hybridize to full-length Gene 1 and are detected following nuclease treatment.
  • the flanking 5' probe 1 also hybridizes to the fusion gene and is detected following nuclease treatment; however the flanking 3' probe 1 does not hybridize to the fusion gene and is hydrolyzed by nuclease treatment.
  • flanking 5' probe 2 and 3' probe 2 can optionally be included in the assay; these hybridize to the full-length gene 2 and are detected following nuclease treatment.
  • the 3' probe 2 also hybridizes to the fusion gene and is detected following nuclease treatment; however the flanking 5' probe 2 does not hybridize to the fusion gene and is hydrolyzed by the nuclease treatment (dotted line).
  • a fusion probe spanning the fusion point can also optionally be included in the assay.
  • the fusion probe hybridizes and is detected following nuclease treatment (solid line).
  • the fusion probe only partially hybridizes to Genes 1 and 2 and at least the non-hybridized portion is hydrolyzed by the nuclease treatment (dotted lines).
  • FIG. 4 is a diagram showing a checkerboard assay detecting Bcr-Abl in vitro transcribed fusion targets with Bcr-Abl fusion probes (Table 4, below). “Yes” indicates detectable signal, “No” indicates lack of detectable signal.
  • FIGS. 5 A and B are schematic diagrams of exemplary methods of capturing one or more fusion probes and/or flanking probes on an array to detect the presence of one or more gene fusions in a single sample.
  • FIG. 5A shows hybridization of a detectably labeled fusion or flanking probe (biotinylated in this case) with a target nucleic acid (step 1), nuclease treatment (step 2), dissociation of the probe from the target nucleic acid (step 3), hybridization of the detectably labeled probe on a microarray including a nucleic acid complementary to the probe (step 4), and detection of the labeled probe (steps 5 and 6).
  • FIG. 5A shows hybridization of a detectably labeled fusion or flanking probe (biotinylated in this case) with a target nucleic acid (step 1), nuclease treatment (step 2), dissociation of the probe from the target nucleic acid (step 3), hybridization of the detectably labeled
  • 5B shows hybridization of a fusion or flanking probe with a target nucleic acid (step 1), nuclease treatment (step 2), dissociation of the probe from the target nucleic acid (step 3), hybridization of the probe on a microarray including a programming linker which is complementary to a portion of the probe (step 4), hybridization with a detection linker, a portion of which is complementary to a different portion of the probe (step 5), hybridization with a detectably labeled nucleic acid (biotinylated in this case) which is complementary to a different portion of the detection linker (step 6), and detection of the labeled nucleic acid (step 7).
  • FIGS. 6A-H are a series of panels showing titration of fusion probes for EML4-ALK-vl (FIG. 6A), EML4-ALK-v2 (FIG. 6B), EML4-ALK-v3a (FIG. 6C), EML4-ALK-v3b-3 (FIG. 6D), EML4-ALK-v4 (FIG. 6E), EML4-ALK-v5a (FIG. 6F), EML4-ALK-v5b-3 (FIG. 6G), and EML4-ALK-v6 (FIG. 6H) with increasing amounts of the corresponding EML4-ALK in vitro transcribed (IVT) RNAs.
  • IVT in vitro transcribed
  • FIGS. 7 A and B are graphs showing signal obtained using the identified ALK flanking probes with full-length ALK IVT (FIG. 7 A) or a truncated ALK IVT (FIG. 7B).
  • nucleic acid and amino acid sequences listed herein or in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. In at least some cases, only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand.
  • SEQ ID NOs: 1-32 are exemplary fusion probe nucleic acid sequences.
  • SEQ ID NOs: 33-132 are exemplary flanking probe nucleic acid sequences.
  • SEQ ID NOs: 133-146 are Bcr-Abl fusion probe nucleic acid sequences.
  • SEQ ID NOs: 147-160 are Bcr-Abl programming linker nucleic acid sequences.
  • SEQ ID Nos: 161-174 are Bcr-Abl detection linker nucleic acid sequences.
  • SEQ ID NO: 175 is an exemplary Bcr-Abl E1A2 fusion region nucleic acid sequence.
  • SEQ ID NO: 176 is an exemplary Bcr-Abl "short overlap" fusion probe nucleic acid sequence.
  • SEQ ID Nos: 177- 184 are exemplary EML4-ALK fusion probe target nucleic acid sequences.
  • SEQ ID Nos: 185-192 are exemplary 5'-ALK flanking probe target nucleic acid sequences.
  • SEQ ID NOs: 193-200 are exemplary 3'-ALK flanking probe target nucleic acid sequences.
  • the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes.
  • the methods include detecting presence of a fusion gene mRNA in a sample from a subject.
  • the methods can include contacting a sample from a subject (such as a sample including nucleic acids) with a fusion probe.
  • the fusion probe includes a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid.
  • the fusion probe is incubated with the sample under conditions sufficient for the fusion probe to specifically hybridize to a gene fusion.
  • the sample is contacted with a nuclease specific for single-stranded nucleic acids (for example, S I nuclease), and the presence of the fusion probe is detected.
  • the fusion gene is identified as present in the sample when the fusion probe is detected.
  • the fusion probe includes a detectable label (such as biotin or horseradish peroxidase) and detecting the presence of the fusion probe includes detecting the detectable label.
  • the fusion probe is detected indirectly, for example by hybridization with a labeled nucleic acid complementary to all or a portion of the fusion probe (e.g., a "programming linker").
  • the fusion probe is detected using a microarray, for example, a microarray including a nucleic acid that is complementary to the fusion probe (see, for example, FIG. 5A).
  • the fusion probe is detected using a microarray including a programming linker complementary to a portion of the fusion probe and subsequently incubating with a detection linker, a portion of which is complementary to a separate portion of the fusion probe.
  • the detection linker can be detectably labeled, or a separate portion of the detection linker can be
  • a detectable label such as biotin or horseradish peroxidase. See, for example, FIG. 5B.
  • the methods include contacting a sample from a subject (such as a sample including nucleic acids) with a fusion probe.
  • the fusion probe includes a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid.
  • the fusion probe is incubated with the sample under conditions sufficient for the fusion probe to specifically hybridize to a gene fusion.
  • the sample is contacted with a nuclease specific for single-stranded nucleic acids (for example, S I nuclease) and the sample is then contacted with a surface including at least two spatially discrete regions, wherein at least one region includes an anchor in association with a bifunctional linker under conditions sufficient for the fusion probe to specifically bind (e.g., hybridize to) the bifunctional linker and detecting the hybridized fusion probe.
  • the bifunctional linker has a first portion specific for (e.g., complementary to) the anchor and a second portion specific for (e.g., complementary to) the fusion probe.
  • the gene fusion is identified as present in the sample when the fusion probe is detected.
  • the methods include detecting presence of more than one gene fusion in a sample from the subject.
  • the methods can include contacting a sample from a subject (such as a sample including nucleic acids) with at least two fusion probes.
  • Each fusion probe includes a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid of a particular (different) gene fusion.
  • the at least two fusion probes are incubated with the sample under conditions sufficient for the fusion probes to specifically hybridize to the gene fusion.
  • the sample is contacted with a nuclease specific for single-stranded nucleic acids (for example, S I nuclease) and the sample is then contacted with a surface including at least two spatially discrete regions including at least one anchor, wherein each anchor is in association with a bifunctional linker which has a first portion specific for (e.g., complementary to) the anchor and a second portion specific for (e.g., complementary to) one of the at least two fusion probes, under conditions sufficient for the fusion probes to bind (e.g., hybridize to) the bifunctional linker, detecting the hybridized fusion probes, and identifying presence of the gene fusion by the spatially distinct region to which the fusion probe is bound.
  • a nuclease specific for single-stranded nucleic acids for example, S I nuclease
  • fusion probes of use in the disclosed methods are about 10-200 nucleotides in length.
  • the fusion probe includes approximately equal numbers of nucleotides from each of the first and second nucleic acids.
  • the fusion probe includes a small number of nucleotides from one of the two nucleic acids and a greater number of nucleotides from the other nucleic acid.
  • the 5' portion of the probe can be about 1- 10 nucleotides in length and the 3' portion of the probe can be about 10 nucleotides or more in length or the 5' portion of the probe can be about 10 nucleotides or more in length and the 3' portion of the probe can be about 1-10 nucleotides in length.
  • the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes.
  • the methods can include contacting a sample from a subject with a first probe complementary to a first nucleic acid 5' to a fusion point between the first nucleic acid and a second nucleic acid under conditions sufficient for the first probe to specifically hybridize to the first nucleic acid and contacting the sample with a second probe complementary to the first nucleic acid 3' to the fusion point between the first and second nucleic acids under conditions sufficient for the second probe to specifically hybridize to the first nucleic acid.
  • the sample is contacted with a nuclease specific for single- stranded nucleic acids (for example, S I nuclease), the presence of the first probe and the second probe is detected, and a ratio of the first probe to the second probe is determined.
  • the fusion gene is identified as present in the sample when the ratio of the first probe to the second probe is different from one (for example, statistically significantly different from one).
  • the gene fusion is detected and does not include a 3' portion of the first nucleic acid if the ratio of the first probe to the second probe is greater than one (for example, statistically significantly greater than one).
  • the gene fusion is detected and does not include a 5' portion of the first nucleic acid if the ratio of the first probe to the second probe is less than one (for example, statistically significantly less than one).
  • the first probe and the second probe are each about 10-200 nucleic acids in length.
  • the first and/or second probes include a detectable label (such as biotin or horseradish peroxidase) and detecting the presence of the probe(s) includes detecting the detectable label.
  • the flanking probes are labeled with the same detectable label.
  • the flanking probes are labeled with different detectable labels.
  • the flanking probes are detected indirectly, for example by hybridization with a labeled nucleic acid complementary to all or a portion of the fusion probe (e.g., a "programming linker").
  • flanking probes are detected using a microarray, for example, a microarray including nucleic acids that are complementary to the flanking probes (see, for example, FIG. 5A).
  • flanking probes are detected using a microarray including
  • the detection linkers can be detectably labeled, or a separate portion of the detection linkers are complementary to additional nucleic acids including a detectable label (such as biotin or horseradish peroxidase). See, for example, FIG. 5B.
  • the methods include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid. These methods further include contacting the sample with a fusion probe that includes a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid, under conditions sufficient for the fusion probe to specifically hybridize to a gene fusion, in addition to contacting the sample with the first probe and the second probe as above.
  • the methods can further include detecting the presence of the fusion probe and determining a ratio of the fusion probe to the first probe and/or a ratio of the fusion probe to the second probe.
  • the methods include contacting a sample from a subject (such as a sample including nucleic acids) with two or more probes that flank the point of fusion between two nucleic acids or genes.
  • the methods can include contacting a sample from a subject with a first probe complementary to a first nucleic acid 5' to a fusion point between the first nucleic acid and a second nucleic acid under conditions sufficient for the first probe to specifically hybridize to the first nucleic acid and contacting the sample with a second probe complementary to the first nucleic acid 3' to the fusion point between the first and second nucleic acids under conditions sufficient for the second probe to specifically hybridize to the first nucleic acid.
  • the sample is contacted with a nuclease specific for single- stranded nucleic acids (for example, S I nuclease) and the sample is then contacted with a surface including at least two spatially discrete regions including at least one anchor, wherein each anchor is in association with a bifunctional linker which has a first portion specific for (e.g., complementary to) the anchor and a second portion specific for (e.g., complementary to) one of the at least flanking probes, under conditions sufficient for the flanking probes to bind (e.g., hybridize to) the bifunctional linker, detecting the hybridized flanking probes, and determining a ratio of the first probe to the second probe.
  • the gene fusion is identified as present in the sample when the ratio of the first probe to the second probe is different from one (for example, statistically significantly different from one).
  • a nuclease protection step can reduce the need for extensive handling of nucleic acids, particularly RNA, which can be sensitive to degradation by contaminating nucleases and thus difficult to work with.
  • embodiments in which nucleic acid purification (before or after probe hybridization) is not required decrease interassay variability introduced by nucleic acid extraction steps.
  • lysis-only embodiments permit the ability to measure both soluble nucleic acids as well as cross-linked nucleic acids (for example in FFPE sections).
  • Nuclease protection of a sample can allow for greater sensitivity and reproducibility in an assay.
  • the methods result in decreased background, for example, because nuclease treatment destroys most non- specifically hybridized nucleic acids.
  • the disclosed assays can be sensitive enough such that amplification of the gene fusion is not necessary in order to detect a signal.
  • Particular method embodiments specifically do not include an amplification (e.g., PCR amplification) step. This reduces drawbacks of an amplification step, such as sequence-specific artifacts or bias, limited dynamic range, and the necessity for using purified and intact nucleic acids.
  • the increased sensitivity of the disclosed methods allow for multiple assays to be performed on a single sample (for example, a single FFPE section can be divided into multiple tests). Furthermore, the increased sensitivity of the assay allows for single copy gene detection in as few as 1000 cells.
  • the disclosed methods are amenable to multiplexing, for example, using a microarray.
  • Particular microarray embodiments are discussed in Section V, below. This allows screening or detection of multiple gene fusions simultaneously (such as detecting the same fusion in many samples, or detecting multiple different gene fusions in a single sample), for example at least 10, at least 25, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, or more gene fusions in a single assay.
  • the multiplex microarray embodiment results in capture of fusion probes at spatially distinct locations, therefore the fusion probes can be detected using the same detectable label and distinguished based on their position in the microarray.
  • nucleic acid molecules consist of nitrogenous bases that are either pyrimidines (cytosine (C), uracil (U), and thymine (T)) or purines (adenine (A) and guanine (G)). These nitrogenous bases form hydrogen bonds between a pyrimidine and a purine, and the bonding of the pyrimidine to the purine is referred to as "base pairing.” More specifically, A will hydrogen bond to T or U, and G will bond to C. "Complementary” refers to the base pairing that occurs between two distinct nucleic acids or two distinct regions of the same nucleic acid.
  • Specifically hybridizable and “specifically complementary” are terms that indicate a sufficient degree of complementarity such that stable and specific binding occurs between the probe (or its analog) and the nucleic acid target (e.g., DNA or RNA).
  • the probe or analog may, but need not have 100% complementarity to its target sequence to be specifically hybridizable.
  • a probe or analog is specifically hybridizable when there is a sufficient degree of complementarity to avoid nonspecific binding of the probe or analog to non-target sequences under conditions where specific binding is desired, for example in the methods disclosed herein. Such binding is referred to as specific hybridization.
  • Placement in direct physical association includes both in solid and liquid form.
  • contacting can occur in vitro with a nucleic acid probe and biological sample in solution or on a surface.
  • Detect To determine if an agent (such as a signal, particular nucleotide, amino acid, nucleic acid molecule, and/or organism) is present or absent, for example a gene fusion nucleic acid. In some examples, this can further include quantification. For example, use of the disclosed methods and probes in particular examples permits detection of a gene fusion in a sample.
  • an agent such as a signal, particular nucleotide, amino acid, nucleic acid molecule, and/or organism
  • Detectable label A compound or composition that is conjugated directly or indirectly to another molecule (such as a nucleic acid molecule, for example a fusion probe, a flanking probe, or a detection probe) to facilitate detection of that molecule.
  • a nucleic acid molecule for example a fusion probe, a flanking probe, or a detection probe
  • labels include fluorescent and fluorogenic moieties, chromogenic moieties, haptens, affinity tags, and radioactive isotopes.
  • the label can be directly detectable (e.g., optically detectable) or indirectly detectable (for example, via interaction with one or more additional molecules that are in turn detectable). Exemplary labels in the context of the probes disclosed herein are described below.
  • Gene Fusion A hybrid gene formed from two or more previously separate genes. Gene fusions can occur as the result of a chromosomal rearrangement, such as a translocation, interstitial deletion, or chromosomal inversion.
  • the "fusion point” or “breakpoint” of a gene fusion is the point of transition between the sequence from the first gene in the fusion to the sequence from the second gene in the fusion.
  • gene fusion and “fusion gene” are used interchangeably herein and indicate the products of a chromosomal rearrangement, including but not limited to DNA (such as genomic DNA or cDNA), RNA, (including mRNA), or protein.
  • Hybridization The ability of complementary single-stranded DNA, RNA, or DNA/RNA hybrids to form a duplex molecule (also referred to as a hybridization complex). Nucleic acid hybridization techniques can be used to form hybridization complexes between a nucleic acid probe, and the gene it is designed to target. In particular non-limiting examples, nucleic acid probes are optimized to target the individual genes or gene fusions listed in Table 1.
  • Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (such as the Na + concentration) of the hybridization buffer will determine the stringency of hybridization. Calculations regarding hybridization conditions for attaining particular degrees of stringency are discussed in Sambrook et al., (1989) Molecular Cloning, second edition, Cold Spring Harbor Laboratory, Plain view, NY (chapters 9 and 11).
  • Nuclease An enzyme that cleaves a phosphodiester bond.
  • An endonuclease is an enzyme that cleaves an internal phosphodiester bond in a nucleotide chain (in contrast to exonucleases, which cleave a phosphodiester bond at the end of a nucleotide chain).
  • Some nucleases have both endonuclease and exonuclease activities.
  • Endonucleases include restriction endonucleases or other site-specific endonucleases (which cleave DNA at sequence specific sites), DNase I, Bal 31 nuclease, S I nuclease, Mung bean nuclease, Ribonuclease A, Ribonuclease Tl, RNase I, RNase PhyM, RNase U2, RNase CLB, micrococcal nuclease, and apurinic/apyrimidinic endonucleases.
  • Exonucleases include exonuclease III and exonuclease VII.
  • a nuclease is specific for single-stranded nucleic acids, such as S I nuclease, Mung bean nuclease, Ribonuclease A, or Ribonuclease Tl .
  • Nucleic acid A deoxyribonucleotide or ribonucleotide polymer in either single or double stranded form, and unless otherwise limited, encompassing analogs of natural nucleotides that hybridize to nucleic acids in a manner similar to naturally occurring nucleotides.
  • the term "nucleotide” includes, but is not limited to, a monomer that includes a base (such as a pyrimidine, purine or synthetic analogs thereof) linked to a sugar (such as ribose, deoxyribose or synthetic analogs thereof), or a base linked to an amino acid, as in a peptide nucleic acid (PNA).
  • a base such as a pyrimidine, purine or synthetic analogs thereof
  • sugar such as ribose, deoxyribose or synthetic analogs thereof
  • PNA peptide nucleic acid
  • nucleotide also includes a locked nucleic acid (LNA).
  • LNA locked nucleic acid
  • a nucleotide is one monomer in a polynucleotide.
  • a nucleotide sequence refers to the sequence of bases in a polynucleotide.
  • Probe A nucleic acid molecule that is capable of hybridizing with a target nucleic acid molecule (e.g., genomic DNA, cDNA, RNA, or mRNA target nucleic acid molecule) and, after hybridization to the target, is capable of being detected either directly or indirectly.
  • a target nucleic acid molecule e.g., genomic DNA, cDNA, RNA, or mRNA target nucleic acid molecule
  • probes permit the detection, and in some examples quantification, of a target nucleic acid molecule, such as a gene fusion nucleic acid molecule or a nucleic acid molecule that is involved in a gene fusion event.
  • a probe includes a detectable label.
  • probes can include one or more peptide nucleic acids and/or one or more locked nucleic acids.
  • a probe is capable of hybridizing with sequences including one or more variations from a "wild type" sequence or portion of a sequence (for example in a gene fusion).
  • a probe may include a sequence having at least 90% identity (such as 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identity) with a "wild type" gene sequence.
  • a "fusion probe” is a probe that includes nucleic acid sequences capable of hybridizing with sequences from two separate genes when the two genes are part of a gene fusion.
  • a fusion probe includes a 5' portion capable of hybridizing with a first nucleic acid (for example from a first gene) and a 3' portion capable of hybridizing with a second nucleic acid (for example, from a second gene), wherein the fusion probe spans the point where the first gene and the second gene are fused (the "fusion point").
  • a "flanking probe” is a probe that includes nucleic acid sequences capable of hybridizing with a single nucleic acid and located 5 Or 3' to a fusion point.
  • a 5' flanking probe includes a probe capable of hybridizing with a portion of a nucleic acid 5' to a fusion point and a 3' flanking probe includes a probe capable of hybridizing with a portion of a nucleic acid 3' to a fusion point.
  • Sample A biological specimen containing DNA (for example, genomic DNA
  • DNA or cDNA DNA or cDNA
  • RNA including mRNA
  • protein or combinations thereof, obtained from a subject.
  • examples include, but are not limited to cells, cell lysates, chromosomal preparations, peripheral blood, urine, saliva, tissue biopsy (such as a tumor biopsy or lymph node biopsy), surgical specimen, bone marrow,
  • a sample includes RNA, such as mRNA.
  • samples are used directly (e.g., fresh or frozen), or can be manipulated prior to use, for example, by fixation (e.g., using formalin) and/or embedding in wax (such as formalin-fixed paraffin-embedded (FFPE) tissue samples).
  • fixation e.g., using formalin
  • FFPE formalin-fixed paraffin-embedded
  • Sequence identity/similarity The identity/similarity between two or more nucleic acid sequences, or two or more amino acid sequences, is expressed in terms of the identity or similarity between the sequences. Sequence identity can be measured in terms of percentage identity; the higher the percentage, the more identical the sequences are. Homologs or orthologs of nucleic acid or amino acid sequences possess a relatively high degree of sequence identity/similarity when aligned using standard methods. Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith &
  • BLAST Basic Local Alignment Search Tool
  • NCBI National Center for Biological Information
  • blastp blastn
  • blastx blastx
  • tblastn tblastx
  • Additional information can be found at the NCBI web site.
  • the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is present in both sequences.
  • the percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100.
  • nucleic acid probes disclosed herein are not limited to the exact sequences shown, as those skilled in the art will appreciate that changes can be made to a sequence, and not substantially affect the ability of a probe to function as desired. For example, sequences having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, such as 100% sequence identity to the disclosed probes are provided herein.
  • sequence identity ranges are provided for guidance only; it is possible that probes can be used that fall outside these ranges.
  • Subject Any organism having a genome, including viruses, single-celled organisms (such as bacteria or yeast), or multi-cellular invertebrate or vertebrate organisms (such as human and non-human mammals).
  • a subject is known or suspected of having a tumor associated with a gene fusion.
  • the methods utilize a fusion probe that spans the point of fusion between two nucleic acids or genes.
  • a sample is contacted with the fusion probe and treated with a nuclease specific for single- stranded nucleic acids. Only probe that is hybridized and thereby forms a duplex with to the target gene (e.g., a nucleic acid having the target gene fusion) will survive nuclease treatment and be subsequently detected.
  • FIG. 1 is a schematic diagram showing exemplary wild-type and fusion genes and an exemplary fusion probe. When the gene fusion is present in a sample, the fusion probe hybridizes and is detected following nuclease treatment (solid line).
  • the fusion probe When the gene fusion is not present in a sample, the fusion probe only partially hybridizes to Genes 1 and 2 and any portion of the fusion probe that is not duplexed with a target is hydrolyzed by the nuclease treatment. In some examples, the portion of the fusion probe that is duplexed to Gene 1 or Gene 2 survives nuclease treatment, but is not detected (for example, because the detectable portion of the probe is hydrolyzed).
  • the methods can include contacting a sample (such as a sample including nucleic acids, for example a sample from a subject) with a fusion probe that has a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid.
  • the probe is incubated with the sample under conditions sufficient for the fusion probe to specifically hybridize to a gene fusion.
  • the sample is contacted with a nuclease specific for single-stranded nucleic acids (for example, S I nuclease), and the presence of the fusion probe detected.
  • the fusion gene is identified as present in the sample when the fusion probe is detected.
  • the first nucleic acid and the second nucleic acid are mRNA (for example, the gene fusion nucleic acid detected is mRNA).
  • the disclosed methods are amenable to multiplexing. This allows screening or detection of multiple gene fusions simultaneously (such as detecting the same fusion in many samples, or detecting multiple different gene fusions in a single sample), for example at least 2, at least 5, at least 10, at least 25, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, or more gene fusions in a single assay.
  • fusion probes specific for two or more distinct gene fusions can be included in the assay.
  • the same probe is used for multiple samples and the identity of the sample is based on sample location (for example, position on a microarray).
  • the fusion probes can be labeled (directly or indirectly) with different detectable labels in order to identify the gene fusions.
  • the fusion probes can be labeled (directly or indirectly) with the same label and their identity can be determined based on their spatial position (for example in a microarray).
  • a fusion probe can specifically hybridize to a gene fusion, such as a gene fusion present in a sample from a subject. For example, one of skill in the art can determine experimentally the features (such as length, base composition, and degree of complementarity) that will enable a nucleic acid (e.g., a fusion probe) to hybridize to another nucleic acid (e.g., a gene fusion nucleic acid) under conditions of selected stringency, while minimizing non-specific hybridization to other substances or molecules.
  • features such as length, base composition, and degree of complementarity
  • nucleic acid sequence of a fusion probe will have sufficient complementarity to the corresponding gene fusion to enable it to hybridize under selected stringent hybridization conditions, for example hybridization at about 37°C or higher (such as about 37°C, 42°C, 50°C, 55°C, 60°C, 65°C, 70°C, 75°C, or higher).
  • hybridization reaction parameters which can be varied are salt concentration, buffer, pH, temperature, time of incubation, amount and type of denaturant such as formamide.
  • nucleic acid e.g.
  • a fusion probe can be added to a sample at a concentration ranging from about 10 pM to about 10 nM (such as about 30 pM to 5 nM, about 100 pM to about 1 nM), in a buffer such as, for example, 6X SSPE-T (0.9 M NaCl, 60 mM NaH 2 P0 4 , 6 mM EDTA, and 0.05% Triton X- 100) or lysis buffer (described below).
  • the probe is added to the sample at a final concentration of about 30 pM.
  • the probe is added to the sample at a final concentration of about 167 pM.
  • the probe is added to the sample at a final concentration of about 1 nM.
  • the nucleic acids in the sample are denatured (for example at about 95°C to about 105°C for about 5- 15 minutes) and hybridized to a gene fusion for between about 10 minutes and about 24 hours (for example, at least about 1 hour to 20 hours, or about 6 hours to 16 hours) at a temperature ranging from about 4°C to about 70°C (for example, about 37°C to about 65°C, about 45°C to about 60°C, or about 50°C to about 60°C).
  • the fusion probe is incubated with the sample at a temperature of at least about 40°C, at least about 45°C, at least about 50°C, at least about 55°C, at least about 60°C, at least about 65°C, or at least about 70°C.
  • the fusion probe is incubated with the sample at about 60°C. In another example, the fusion probe is incubated with the sample at about 50°C.
  • These hybridization temperatures are exemplary, and one of skill in the art can select appropriate hybridization temperature depending on factors such as the length and nucleotide composition of the fusion probe.
  • the methods do not include nucleic acid purification
  • nucleic acid purification is not performed prior to contacting the sample with the fusion probe and/or nucleic acid purification is not performed following contacting the sample with the fusion probe).
  • no preprocessing of the sample is required except for cell lysis.
  • cell lysis and contacting the sample with the fusion probe occur sequentially. In other examples, cell lysis and contacting the sample with the fusion probe occur concurrently, in some non-limiting examples without any intervening steps.
  • the sample is subjected to a nuclease protection procedure. Fusion probes which have hybridized to a gene fusion are not hydrolyzed by the nuclease and can be subsequently detected.
  • nucleases Treatment with one or more nucleases will destroy nucleic acid molecules other than the fusion probes which have hybridized to a gene fusion nucleic acid present in the sample. For example, if the sample includes a cellular extract or lysate, unwanted nucleic acids, such as genomic DNA, cDNA, tRNA, rRNA and mRNAs other than the gene fusion of interest and portions of the gene fusion of interest that are not hybridized to complementary probe sequences, can be substantially destroyed in this step. Any of a variety of nucleases can be used, including, pancreatic RNAse, mung bean nuclease, S 1 nuclease, RNAse A,
  • Ribonuclease Tl Exonuclease III, Exonuclease VII, RNAse CLB, RNAse PhyM, RNAse U2, or the like, depending on the nature of the hybridized complexes and of the undesirable nucleic acids present in the sample.
  • One of skill in the art can select an appropriate nuclease, for example based on whether DNA or RNA is to be detected.
  • the nuclease is specific for single- stranded nucleic acids, for example SI nuclease.
  • SI nuclease is commercially available from for example, Promega, Madison, WI (cat. no. M5761); Life Technologies/Invitrogen, Carlsbad, CA (cat. no. 18001-016); Fermentas, Glen Burnie, MD (cat. no. EN0321), and others. Reaction conditions for these enzymes are well-known in the art and can be optimized empirically.
  • SI nuclease diluted in an appropriate buffer such as 0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.0225 M ZnS0 4 , 0.05% KATHON
  • an appropriate buffer such as 0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.0225 M ZnS0 4 , 0.05% KATHON
  • the samples optionally are treated to otherwise remove non-hybridized material and/or to inactivate or remove residual enzymes (e.g., by phenol extraction, precipitation, column filtration, etc.).
  • the samples are optionally treated to dissociate the target nucleic acid (such as target gene fusion or target full length or wild type gene) from the probe (e.g., using base hydrolysis and heat).
  • the hybridized target can be degraded, e.g. , by nucleases or by chemical treatments, leaving the fusion probe in direct proportion to how much probe had been hybridized to target.
  • the sample can be treated so as to leave the (single strand) hybridized portion of the target, or the duplex formed by the hybridized target and the probe, to be further analyzed.
  • the presence of the fusion probe is then detected.
  • Any suitable method can be used to detect the fusion probe following hybridization and nuclease treatment.
  • the fusion probe includes a detectable label and detecting the presence of the fusion probe includes directly detecting the detectable label.
  • the fusion probe is detected indirectly, for example by hybridization with a labeled nucleic acid.
  • the fusion probe is detected using a microarray, for example, a microarray including a detectably labeled nucleic acid (for example labeled with biotin or horseradish peroxidase) that is complementary to the fusion probe (see, for example, FIG. 5A).
  • the fusion probe is detected using a microarray including a programming linker complementary to a portion of the fusion probe and subsequently incubating with a detection linker, a portion of which is complementary to a separate portion of the fusion probe.
  • the detection linker can be detectably labeled, or a separate portion of the detection linker is complementary to an additional nucleic acid including a detectable label (such as biotin or horseradish peroxidase). See, for example, FIG. 5B.
  • a detectable label such as biotin or horseradish peroxidase
  • fusion probes of use in the disclosed methods are about 10-200 nucleotides in length. In some embodiments, fusion probes of use in the disclosed methods are no more than 500, no more than 400, no more than 300, or no more than 200 nucleotides in length, such as 20 to 100 nucleotides in length. In some examples, the fusion probe includes approximately equal numbers of nucleotides from each of the first and second nucleic acids. Fusion probes are discussed in more detail in Section VIB, below.
  • the fusion probe includes a small number of nucleotides complementary to one of the two nucleic acids (a "short overlap") and a greater number of nucleotides from the other nucleic acid.
  • the "short overlap" portion of the fusion probe also includes a detectable label (such as biotin, fluorescein or other fluorescent molecules, digoxigenin, or dinitrophenol).
  • the fusion probe can be end-labeled (for example, the detectable label is included at the 5 Or 3' end of the probe) or the detectable label can be included at one or more internal positions of the fusion probe.
  • FIG. 2 is a schematic diagram showing exemplary wild-type and fusion genes and an exemplary direct-labeled fusion probe having a four nucleotide overlap with the 5' portion of the fusion gene.
  • the label biotin in this example
  • the label is located at or near the 5' end of the probe (for example at the 5' end or in the "short overlap" portion of the probe).
  • the fusion probe hybridizes and the label is detected following nuclease treatment (top panel).
  • the fusion probe does not hybridize to Gene 1 and is hydrolyzed by the nuclease treatment (middle panel).
  • the fusion probe hybridizes to Gene 2, however the 5' end including the label does not hybridize and is cleaved by the nuclease treatment (bottom panel). Therefore, the labeled probe is only detected in samples where the gene fusion is present.
  • the 5' portion of the probe can be about 1-10 nucleotides in length and the 3' portion of the probe can be about 10-200 nucleotides or more in length or the 5' portion of the probe can be about 10-200 nucleotides or more in length and the 3' portion of the probe can be about 1-10 nucleotides in length.
  • Short overlap fusion probes are discussed in more detail in Section VIB, below.
  • FIG. 3 is a schematic diagram showing exemplary wild type and fusion genes and exemplary flanking probes and (an optional exemplary fusion probe).
  • the fusion gene includes a 5' portion of Gene 1 and a 3' portion of Gene 2 (middle panel).
  • the flanking 5' probe 1 and 3' probe 1 hybridize to the full-length (e.g., wild type) Gene 1 and are detected following nuclease treatment (top panel).
  • the flanking 5' probe 1 also hybridizes to the fusion gene and is detected following nuclease treatment (middle panel); however the flanking 3' probe 1 does not hybridize to the fusion gene and is hydrolyzed by nuclease treatment (middle panel).
  • the flanking 5' probe 2 and 3' probe 2 can optionally be included in the assay; these hybridize to the full-length (e.g., wild type) Gene 2 and are detected following nuclease treatment (bottom panel).
  • the 3' probe 2 also hybridizes to the fusion gene and is detected following nuclease treatment; however the flanking 5' probe 2 does not hybridize to the fusion gene and is hydrolyzed by the nuclease treatment (middle panel).
  • a fusion probe spanning the fusion point can also optionally be included in the assay.
  • the fusion probe hybridizes and is detected following nuclease treatment (solid line).
  • the fusion probe only partially hybridizes to Genes 1 and 2 and is hydrolyzed by the nuclease treatment (dotted lines).
  • the portion of the fusion probe that is duplexed to Gene 1 or Gene 2 remains, but is not detected (for example, because the detectable portion of the probe is hydrolyzed).
  • the methods can include contacting a sample from a subject with a first probe complementary to a first nucleic acid 5' to a fusion point between the first nucleic acid and a second nucleic acid under conditions sufficient for the first probe to specifically hybridize to the first nucleic acid, contacting the sample with a second probe complementary to the first nucleic acid 3' to the fusion point between the first and second nucleic acids under conditions sufficient for the second probe to specifically hybridize to the first nucleic acid, contacting the sample with a nuclease specific for single-stranded nucleic acids (for example, S I nuclease), detecting presence of the first probe and the second probe, and determining a ratio of the first probe to the second probe.
  • a nuclease specific for single-stranded nucleic acids for example, S I nuclease
  • the fusion gene is identified as present in the sample when the ratio of the first probe to the second probe is different from one (for example, statistically significantly different from one).
  • the gene fusion is detected and does not include a 3' portion of the first nucleic acid if the ratio of the first probe to the second probe is greater than one (for example, statistically significantly greater than one).
  • the gene fusion is detected and does not include a 5' portion of the first nucleic acid if the ratio of the first probe to the second probe is less than one (for example, statistically
  • the first nucleic acid and the second nucleic acid are mRNA (for example, the gene fusion nucleic acid detected is mRNA).
  • the methods include determining a ratio of the second probe to the first probe.
  • the gene fusion is detected and does not include a 5' portion of the first nucleic acid if the ratio of the second probe to the first probe is greater than one (for example, statistically significantly greater than one).
  • the gene fusion is detected and does not include a 3' portion of the first nucleic acid if the ratio of the second probe to the first probe is less than one (for example, statistically significantly less than one).
  • the first probe and the second probe are each about 10-200 nucleic acids in length.
  • the sample is contacted with two or more probes that are complementary to the first nucleic acid 5' to the fusion point and/or contacted with two or more probes that are complementary to the first nucleic acid 3' to the fusion point.
  • the sample is contacted with one or more probes that are complementary to the first nucleic acid in the gene fusion (for example at least one 5' flanking probe and at least one 3' flanking probe) and one or more probes that are complementary to the second nucleic acid in the gene fusion (for example, at least one 5' flanking probe and at least one 3' flanking probe).
  • the sample is contacted with one or more 5' and 3' flanking probes complementary to a first or second nucleic acid in a gene fusion and one or more 5' and 3' flanking probes complementary to a first or second nucleic acid in a different gene fusion.
  • the probes can be labeled with different detectable labels or can be labeled with the same detectable label and distinguished based on spatial
  • the disclosed methods are amenable to multiplexing. This allows screening or detection of multiple gene fusions simultaneously (such as detecting the same fusion in many samples, or detecting multiple different gene fusions in a single sample), for example at least 2, at least 5, at least 10, at least 25, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 750, at least 1000, or more gene fusions in a single assay.
  • 5' and 3' flanking probes specific for two or more distinct gene fusions can be included in the assay.
  • flanking probes are used for multiple samples and the identity of the sample is based on sample location (for example, position on a microarray).
  • the flanking probes can be labeled (directly or indirectly) with different detectable labels in order to identify the gene fusions.
  • the flanking probes can be labeled (directly or indirectly) with the same label and their identity can be determined based on their spatial position (for example in a microarray).
  • a probe such as a 5' flanking probe and a 3' flanking probe
  • a nucleic acid such as a full-length and/or gene fusion nucleic acid present in a sample from a subject.
  • a nucleic acid such as a full-length and/or gene fusion nucleic acid present in a sample from a subject.
  • one of skill in the art can determine experimentally the features (such as length, base composition, and degree of complementarity) that will enable a nucleic acid (e.g., a flanking probe) to hybridize to another nucleic acid (e.g., a full-length or a gene fusion nucleic acid) under conditions of selected stringency, while minimizing non-specific hybridization to other substances or molecules.
  • nucleic acid sequence of a flanking probe will have sufficient complementarity to the corresponding full-length gene and the gene fusion to enable it to hybridize under selected stringent hybridization conditions, for example hybridization at about 37°C or higher (such as about 37°C, 42°C, 50°C, 55°C, 60°C, 65°C, 70°C, 75°C, or higher).
  • hybridization reaction parameters which can be varied are salt concentration, buffer, pH, temperature, time of incubation, amount and type of denaturant such as formamide.
  • nucleic acid e.g.
  • a flanking probe can be added to a sample at a concentration ranging from about 10 pM to about 10 nM (such as about 30 pM to 5 nM, about 100 pM to about 1 nM), in a buffer such as, for example, 6X SSPE-T (0.9 M NaCl, 60 mM NaH 2 P0 4 , 6 mM EDTA, and 0.05% Triton X-100) or lysis buffer (described below).
  • the probe is added to the sample at a final concentration of about 30 pM.
  • the probe is added to the sample at a final concentration of about 167 pM.
  • the probe is added to the sample at a final concentration of about 1 nM.
  • the nucleic acids in the sample are denatured (for example at about 95°C to about 105°C for about 5- 15 minutes) and hybridized to a gene fusion for between about 10 minutes and about 24 hours (for example, at least about 1 hour to 20 hours, or about 6 hours to 16 hours) at a temperature ranging from about 4°C to about 70°C (for example, about 37°C to about 65°C, about 45°C to about 60°C, or about 50°C to about 60°C).
  • the flanking probes are incubated with the sample at a temperature of at least about 40°C, at least about 45°C, at least about 50°C, at least about 55°C, at least about 60°C, at least about 65°C, or at least about 70°C. In one example, the flanking probes are incubated with the sample at about 60°C. In another example, the flanking probes are incubated with the sample at about 50°C.
  • These hybridization temperatures are exemplary, and one of skill in the art can select appropriate hybridization temperature depending on factors such as the length and nucleotide composition of the flanking probes.
  • the methods do not include nucleic acid purification (for example, nucleic acid purification is not performed prior to contacting the sample with the flanking probes and/or nucleic acid purification is not performed following contacting the sample with the flanking probes).
  • nucleic acid purification is not performed prior to contacting the sample with the flanking probes and/or nucleic acid purification is not performed following contacting the sample with the flanking probes.
  • no pre-processing of the sample is required except for cell lysis.
  • cell lysis and contacting the sample with the flanking probes occur sequentially.
  • cell lysis and contacting the sample with the flanking probes occur concurrently, in some non-limiting examples without any intervening steps.
  • the sample is subjected to a nuclease protection procedure. Flanking probes which have hybridized to a full-length nucleic acid or a gene fusion are not hydrolyzed by the nuclease and can be subsequently detected.
  • nucleic acid molecules other than the flanking probes which have hybridized to a full-length or gene fusion nucleic acid present in the sample will destroy nucleic acid molecules other than the flanking probes which have hybridized to a full-length or gene fusion nucleic acid present in the sample.
  • unwanted nucleic acids such as genomic DNA, cDNA, tRNA, rRNA and mRNAs other than the gene or gene fusion of interest and portions of the gene fusion of interest that are not hybridized to complementary probe sequences, can be substantially destroyed in this step.
  • nucleases Any of a variety of nucleases can be used, including, pancreatic RNAse, mung bean nuclease, S I nuclease, RNAse A, Ribonuclease Tl , Exonuclease III, Exonuclease VII, RNAse CLB, RNAse PhyM, RNAse U2, or the like, depending on the nature of the hybridized complexes and of the undesirable nucleic acids present in the sample.
  • the nuclease is specific for single-stranded nucleic acids, for example S I nuclease.
  • An advantage of using a nuclease specific for single- stranded nucleic acids in some method embodiments disclosed here is to remove such single-stranded ("sticky") molecules from subsequent reaction steps where they may lead to unnecessary background or cross -reactivity.
  • S I nuclease is commercially available from for example, Promega, Madison, WI (cat. no. M5761); Life Technologies/Invitrogen, Carlsbad, CA (cat. no. 18001-016); Fermentas, Glen Burnie, MD (cat. no. EN0321), and others. Reaction conditions for these enzymes are well-known in the art and can be optimized empirically.
  • S I nuclease diluted in an appropriate buffer such as a buffer including sodium acetate, sodium chloride, zinc sulfate, and detergent, for example, 0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.0225 M ZnS0 4 , 0.05% KATHON
  • an appropriate buffer such as a buffer including sodium acetate, sodium chloride, zinc sulfate, and detergent, for example, 0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.0225 M ZnS0 4 , 0.05% KATHON
  • the samples optionally are treated to otherwise remove unhybridized material and/or to inactivate or remove residual enzymes (e.g., by phenol extraction, precipitation, column filtration, etc.).
  • the samples are optionally treated to dissociate the target nucleic acid (such as target gene fusion or target full length or wild type gene) from the probe (e.g., using base hydrolysis and heat).
  • the hybridized target can be degraded, e.g., by nucleases or by chemical treatments, leaving the flanking probes in direct proportion to how much probe had been hybridized to target.
  • the sample can be treated so as to leave the (single strand) hybridized portion of the target, or the duplex formed by the hybridized target and the probe, to be further analyzed.
  • flanking probes The presence of the flanking probes in the sample is then detected and a ratio of the first probe (5' flanking probe) to the second probe (3' flanking probe) is determined.
  • the presence of a gene fusion in the sample is detected if the ratio of the 5' flanking probe to the 3' flanking probe is different from one (for example, statistically significantly different from one).
  • the effect of a gene fusion on the ratio of 5' and 3' flanking probes depends on whether the flanking probes are complementary to the 5' gene in the fusion (Gene 1 in FIG. 3) or the 3' gene in the fusion (Gene 2 in FIG. 3).
  • the first and second probes are complementary to the 5' gene in the fusion.
  • the gene fusion is detected and does not include a 3' portion of the nucleic acid (Gene 1) if the ratio of the first probe to the second probe is greater than one (for example, statistically significantly greater than one).
  • the gene fusion is present and does not include a 3' portion of the nucleic acid if the ratio is about at least 1.1, such as at least 1.5, at least 1.8, at least 2, at least 2.5, at least 3, at least 4, at least 5, at least 10 or at least 20, for example 1.1 to 20 or 1.1 to 60, such as 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0, 3.5, 4.0, .4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 330, 40, 50, 60, or more.
  • a gene fusion is present and does not include a 3' portion of the nucleic acid if the ratio is about at least 1.5. In other examples, a gene fusion is present and does not include a 3' portion of the nucleic acid if the ratio is about at least 1.8. In other examples, the gene fusion is detected and does not include a 5' portion of the nucleic acid (gene 1) if the ratio of the first probe to the second probe is less than one (for example, statistically significantly less than one).
  • the gene fusion is present and does not include a 5' portion of the nucleic acid if the ratio is no more than 0.95, such as no more than 0.9, no more than 0.8, no more than 0.7, no more than 0.6, no more than 0.5, or no more than 0.1, for example 0.05 to 0.95, such as about 0.95, 0.9, 0.85, 0.8, 0.75, 0.7, 0.65, 0.6, 0.55, 0.5, 0.45, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, or less.
  • 0.95 such as no more than 0.9, no more than 0.8, no more than 0.7, no more than 0.6, no more than 0.5, or no more than 0.1
  • 0.05 to 0.95 such as about 0.95, 0.9, 0.85, 0.8, 0.75, 0.7, 0.65, 0.6, 0.55, 0.5, 0.45, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, or less.
  • the first and second probes are complementary to the 3' gene in the fusion.
  • the gene fusion is detected and does not include a 3' portion of the nucleic acid if the ratio of the first probe to the second probe is greater than one (for example, statistically significantly greater than one).
  • the gene fusion is present and does not include a 3' portion of the nucleic acid (gene 2) if the ratio is at least 1.1, such as at least 1.5, at least 1.8, at least 2, at least 2.5, at least 3, at least 4, at least 5, at least 10 or at least 20, for example 1.1 to 20 or 1.1 to 60, such as about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0, 3.5, 4.0, .4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, or more.
  • the ratio is at least 1.1, such as at least 1.5, at least 1.8, at least 2, at least 2.5, at least 3, at least 4, at least 5, at least 10 or at least 20, for example 1.1 to 20 or 1.1 to 60, such as about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6,
  • a gene fusion is present and does not include a 5' portion of the nucleic acid if the ratio is about at least 1.5. In other examples, a gene fusion is present and does not include a 3' portion of the nucleic acid if the ratio is about at least 1.8. In other examples, the gene fusion is detected and does not include a 5' portion of the nucleic acid (gene 2) if the ratio of the first probe to the second probe is less than one (for example, statistically significantly less than one).
  • the gene fusion is present and does not include a 3' portion of the nucleic acid if the ratio is no more than 0.95, such as no more than 0.9, no more than 0.8, no more than 0.7, no more than 0.6, no more than 0.5, or no more than 0.1, for example 0.05 to 0.95, such as about 0.95, 0.9, 0.85, 0.8, 0.75, 0.7, 0.65, 0.6, 0.55, 0.5, 0.45, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, or less.
  • 0.95 such as no more than 0.9, no more than 0.8, no more than 0.7, no more than 0.6, no more than 0.5, or no more than 0.1
  • 0.05 to 0.95 such as about 0.95, 0.9, 0.85, 0.8, 0.75, 0.7, 0.65, 0.6, 0.55, 0.5, 0.45, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, or less.
  • the gene fusion is present if the ratio of the flanking probes (for example, the ratio of a 5' flanking probe to a 3' flanking probe or the ratio of a 3' flanking probe to a 5' flanking probe) differs from a control (such as an average ratio in a wild-type sample) by at least two standard deviations (for example, at least 2, 3, 4, 5, or more standard deviations).
  • the control is the ratio (for example the average ratio) of flanking probes in a sample that does not include a gene fusion.
  • the flanking probe ratio when a gene fusion is present may be less than when the RNA or mRNA is normally expressed at lower levels.
  • One of skill in the art can determine the level at which an RNA or mRNA is normally expressed in a cell and determine the range of ratios that are expected to reflect the presence of a gene fusion in the sample.
  • the methods include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.
  • the methods include contacting the sample with a fusion probe including a 5' portion complementary to a first nucleic acid and a 3' portion complementary to a second nucleic acid (such as discussed in Section III, above) under conditions sufficient for the fusion probe to specifically hybridize to a gene fusion, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid in addition to contacting the sample with the first probe and the second probe above.
  • the methods further include detecting presence of the fusion probe and determining a ratio of the fusion probe to the first probe and/or a ratio of the fusion probe to the second probe.
  • the percentage of the gene fusion relative to the full length gene can be determined by determining the ratio of the fusion probe to the first probe (e.g., the 5' flanking probe) or the ratio of the fusion probe to the second probe (e.g., the 3' flanking probe). For example, if the 5' portion of the gene is present in the gene fusion, the ratio of the fusion probe to the 5' flanking probe will be the percentage of the gene fusion nucleic acid present in the sample relative to the full length nucleic acid. Likewise, if the 3' portion of the gene is present in the gene fusion, the ratio of the fusion probe to the 3' flanking probe will be the percentage of the gene fusion nucleic acid present in the sample relative to the full length nucleic acid.
  • the first and/or second probe includes a detectable label and detecting the presence of the probe(s) includes detecting the detectable label.
  • the flanking probes are labeled with the same detectable label.
  • the flanking probes are labeled with different detectable labels.
  • the flanking probes are detected indirectly, for example by hybridization with a labeled nucleic acid.
  • the flanking probes are detected using a microarray, for example, a microarray including nucleic acids that are complementary to the flanking probes (see, for example, FIG. 5A).
  • the flanking probes are detected using a microarray including
  • the detection linkers can be detectably labeled, or a separate portion of the detection linkers are complementary to additional nucleic acids including a detectable label (such as biotin or horseradish peroxidase). See, for example, FIG. 5B. Methods of detecting the probes are provided in greater detail in Section V below.
  • any suitable method of detecting the presence of a nucleic acid (such as a probe) in a sample can be utilized in the disclosed methods.
  • the disclosed probes (such as one or more fusion or flanking probes) are directly labeled.
  • the disclosed probes are detected by hybridization with a detection probe, which has a sequence complementary to at least a portion of the fusion or flanking probe and a detectable label. Detectable labels and methods of incorporating such labels into a nucleic acid molecule such as a probe are well known in the art.
  • nucleic acid probes are labeled with dNTPs covalently attached to hapten molecules (such as a nitro-aromatic compound (e.g.,
  • a label can be directly or indirectly attached to a dNTP at any location on the dNTP, such as a phosphate (e.g., a, ⁇ or ⁇ phosphate) or a sugar.
  • a phosphate e.g., a, ⁇ or ⁇ phosphate
  • the label is a hapten
  • detection of labeled nucleic acid molecules can be accomplished by contacting the hapten-labeled nucleic acid molecules bound to the genomic target sequence with a primary anti-hapten antibody.
  • the primary anti-hapten antibody such as a mouse anti- hapten antibody
  • a secondary anti-antibody such as a goat anti-mouse IgG antibody conjugated to an enzyme is used for signal amplification.
  • the label is biotin and detection is accomplished by contacting the sample with avidin-horseradish peroxidase.
  • a detectable label includes various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or
  • Additional detectable labels include Raman (light scattering) probes.
  • probes are labeled with fluorescent molecules (or fluorochromes).
  • fluorescent molecules or fluorochromes.
  • Numerous fluorochromes are known to those of skill in the art, and can be selected, for example from Life Technologies (formerly Invitrogen), e.g., see, The Handbook— A Guide to Fluorescent Probes and Labeling Technologies.
  • fluorophores examples include thiol-reactive europium chelates which emit at approximately 617 nm (Heyduk and Heyduk, Anal. Biochem. 248:216-27, 1997; J. Biol. Chem.
  • a fluorescent label can also be a fluorescent nanoparticle, such as a semiconductor nanocrystal, e.g., a QUANTUM DOTTM (obtained, for example, from Life
  • the probes are designed such that hybridization of each probe and subsequent nuclease treatment produces a fragment of a specific size.
  • the probes can then be detected (directly or indirectly) utilizing size- separation techniques, such as gel electrophoresis (for example, slab or capillary gel electrophoresis) or liquid chromatography (for example, HPLC).
  • size- separation techniques such as gel electrophoresis (for example, slab or capillary gel electrophoresis) or liquid chromatography (for example, HPLC).
  • the probes can be labeled with different detectable labels (for example different fluors) in order to discriminate fragments that are similar in size.
  • the probes can also be detected utilizing mass spectrometry methods.
  • the disclosed fusion or flanking probes can be labeled with different detectable labels or can be contacted with different detection probes, in order to separately detect each probe if more than one probe is present in a reaction mixture.
  • the presence of one or more probes is detected using a microarray.
  • the fusion and/or flanking probes can be labeled with the same detectable label, and the probes are distinguished based on the spatial location of signal on the microarray.
  • the probes are detected on a microarray using a quantitative nuclease protection assay technique, for example, as described in International Patent Publications WO 99/032663; WO 00/037683; WO 00/037684; WO 00/079008; WO 03/002750; and WO 08/121927; and U.S. Pat. Nos. 6,238,869; 6,458,533; and 7,659,063, incorporated herein by reference in their entirety. See also, Martel et al, Assay and Drug Development Technologies.
  • the solution is neutralized and transferred onto a microarray, such as a programmed ARRAYPLATE (HTG Molecular, Arlington, AZ; each element of the ARRAYPLATE is programmed to capture a specific probe, for example utilizing an anchor attached to the plate and a programming linker associated with the anchor), and the probes are captured during an incubation (for example, overnight at about 50°C).
  • a microarray such as a programmed ARRAYPLATE (HTG Molecular, Arlington, AZ; each element of the ARRAYPLATE is programmed to capture a specific probe, for example utilizing an anchor attached to the plate and a programming linker associated with the anchor), and the probes are captured during an incubation (for example, overnight at about 50°C).
  • the platform can instead be a NIMBLEGEN microarray (Roche Nimblegen, Madison, WI) or the probes can be captured on X-MAP beads (Luminex, Austin, TX), an assay referred to as the QBEAD assay, or processed further, including as desired PCR amplification or ligation reactions, and for instance then measured by sequencing, or by methods such as NANOSTRING).
  • the media is removed and a cocktail of probe- specific detection linkers are added, in the case of the
  • ARRAYPLATE and QBEAD assays which hybridize to their respective (captured) probes during an incubation (for example, 1 hour at about 50°C). See, for example, FIG. 5B.
  • This step is skipped in the case of the NIMBLEGEN microarray assays because the probes are directly biotinylated, and there is no use of detection linker (e.g., FIG. 5A).
  • the array or beads are washed and then a biotin linker (an oligonucleotide that hybridizes to a common sequence on every detection linker, with biotin incorporated into it) is added and incubated (for example, 1 hour at about 50°C).
  • HRP-labeled avidin avidin-HRP
  • avidin-HRP HRP-labeled avidin
  • Substrate is added and the plate is imaged to measure the intensity of every element within the plate.
  • QBEAD Avidin-PE is added, the beads are washed, and then measured by flow cytometry using the Luminex 200, FLEXMAP 3D, or other appropriate instrument.
  • a tyramide signal amplification step is optionally carried out in the presence of substrate, resulting in the deposition of Cy3 labeled probe, the slides are washed, dried, and scanned in a standard microarray scanner.
  • Exemplary programming linkers and detection linkers are provided in Table 6 (Example 1).
  • One of skill in the art can design suitable programming linkers, detection linkers, and other reagents for use in a quantitative nuclease protection assay based upon the fusion probes and/or flanking probes utilized in the methods disclosed herein.
  • HYBRIDdb primaryate.or.kr/hybriddb
  • ChimerDB ChimerDB
  • the disclosed methods include the step of selecting a particular gene fusion, referred to herein as a target gene fusion.
  • fusion probes and/or flanking probes can be designed to be used in the disclosed methods using the criteria set forth herein in combination with the knowledge of one skilled in the art.
  • gene fusions are oncogenic gene fusions. For example, if a subject is known or suspected of having a particular type of tumor, such as chronic myelogenous leukemia or acute myelogenous leukemia, the gene fusion selected can be one that is associated with that tumor (such as a Bcr-Abl gene fusion). Exemplary gene fusions and associated tumors are shown in Table 1. Additional gene fusions include non-oncogenic (e.g., non-transforming gene fusions) and genomic changes that provide a selective advantage (e.g., in pathogens such as viruses and bacteria).
  • probe-target hybridization specificity include probe length, melting temperature, self-complementarity, and the presence of repetitive or non-unique sequence. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Press, 2001; Ausubel et al., Current Protocols in Molecular Biology, Greene Publishing Associates, 1992 (and Supplements to 2000); Ausubel et al., Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 4th ed., Wiley & Sons, 1999.
  • the specificity of a probe increases with length.
  • a probe that includes 30 consecutive nucleotides will anneal to a target sequence with a higher specificity than a corresponding probe of only 15 nucleotides.
  • the fusion and flanking probes disclosed herein can be selected to include at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70 or more consecutive nucleotides complementary to a gene fusion or complementary to a particular nucleic acid molecule.
  • the fusion or flanking probes disclosed herein are not more than 500 nucleotides, such as no more than 400, no more than 300, no more than 250, no more than 200, no more than 100 , or even no more than 50 consecutive nucleotides complementary to a gene fusion or complementary to a particular nucleic acid molecule such as 10 to 500 nucleotides, 10 to 400 nucleotides, 10 to 250 nucleotides, 10 to 200 nucleotides, 10 to 100 nucleotides, 10 to 75 nucleotides, 10 to 60 nucleotides, 40 to 80 nucleotides, 100 to 200 nucleotides, or 10 to 50 consecutive nucleotides complementary to a gene fusion or complementary to a particular nucleic acid molecule (for example a first or second nucleic acid that is part of a gene fusion).
  • a particular nucleic acid molecule for example a first or second nucleic acid that is part of a gene fusion.
  • a probe is at least 10 nucleotides in length, such as at least 10 contiguous nucleotides complementary to a nucleic acid sequence, such as a sequence flanking a gene fusion point or gene fusion nucleic acid sequences disclosed herein.
  • probes having at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, or more contiguous nucleotides complementary to a nucleic acid molecule, for example a first or second nucleic acid that is part of a gene fusion.
  • each nucleic acid probe is at least 30 nucleotides in length. In one non-limiting example, each nucleic acid probe is about 40 nucleotides in length. In a particular example, each nucleic acid probe is about 50 nucleotides in length.
  • Conditions resulting in particular degrees of hybridization will vary depending upon the nature of the hybridization method and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (such as the Na + concentration) of the hybridization buffer will determine the stringency of hybridization.
  • the probes utilized in the disclosed methods have a melting temperature (T m ) of at least about 37°C, at least about 42°C, at least about 45°C, 50°C, at least about 55°C, at least about 60°C, at least about 65°C, at least about 70°C, at least about 75°C, at least about 80°C, such as about 37°C-80°C (for example, about 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80°C).
  • T m melting temperature of at least about 37°C, at least about 42°C, at least about 45°C, 50°C, at least about 55°C, at least about 60
  • probes that are degenerate at one or more positions (such as 1,
  • a probe that includes a mixture of nucleotides (such as 2, 3, or 4 nucleotides) at a specified position in the probe.
  • the probes disclosed herein include one or more synthetic bases or alternative bases (such as inosine).
  • the probes disclosed herein include one or more modified nucleotides or nucleic acid analogues, such as one or more locked nucleic acids (see, e.g., U.S. Pat. No. 6,794,499) or one or more peptide nucleic acids.
  • use of one or more locked nucleic acids or peptide nucleic acids in the probe can increase the T m of the probe relative to the T m of a probe of the same length and composition which does not include the modified nucleic acid.
  • the disclosed methods can be used to detect the presence of a gene fusion in a sample from a subject.
  • Gene fusions are well known to one of skill in the art. Gene fusions may produce a gene product with a new or different function than that of either of the two fusion partners.
  • a gene fusion includes an intact or mostly intact gene sequence fused to a promoter from another gene, for example a strong promoter that upregulates expression of the gene sequence.
  • a gene fusion is an oncogene. Table 1 provides exemplary genes involved in gene fusions and exemplary gene fusions. Other gene fusions, including those not yet identified, can be detected by one of skill in the art utilizing the methods disclosed herein.
  • the probe is a fusion probe, which hybridizes to a portion of each gene included in the gene fusion and spans the fusion point.
  • the fusion probe includes at least two parts, such that the 5' portion of the probe is capable of hybridizing to the first gene and the 3' portion of the probe is capable of hybridizing to the second gene.
  • a fusion probe is about 10-200 nucleotides in length (including but not limited to about 20-100, 25-50, or 30-45 nucleotides in length and others as described above) In other examples, a fusion probe is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 14, 150, 160, 170, 180, 190, 200, or more nucleotides in length.
  • the 5' portion and 3' portion of the fusion probe are the same or a similar length (for example, the 5' portion is at least 9 nucleotides long, such as about 9-25 nucleotides long and the 3' portion is at least 9 nucleotides long, such as about 9-25 nucleotides long).
  • the 5' portion of the probe is 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more nucleotides long
  • the 3' portion of the probe is the same number of nucleotides.
  • the 5' portion and the 3' portion are not the same or a similar length.
  • the 5' portion of the probe is 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more nucleotides long
  • the 3' portion of the probe is about 1-20 (such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides shorter or longer than the 5' portion of the probe.
  • the 5' portion of the probe or the 3' portion of the probe is very short, for example about 1-10 nucleotides long, while the other portion of the probe is a length similar to that described above (for example at least 9 nucleotides long, such as about 9-50 nucleotides long).
  • the 5' portion of the probe is at least about 1-10 nucleotides long (such as at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 nucleotides long) and the 3' portion of the probe is about at least 9 nucleotides long, such as at least about 9-50 nucleotides long (such as at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 , 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides).
  • the 3' portion of the probe is at least about 1-10 nucleotides long (such as at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 nucleotides long) and the 5' portion of the probe is about at least 9 nucleotides long, such as at least about 9-50 nucleotides long (such as at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 , 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides).
  • the 5' portion of the probe is about 1-3 bases long and the 3' portion of the probe is at least about 10 nucleotides long (such as at least about 10-200, at least about 10-100, or at least about 10-50 nucleotides long) or vice versa. In other examples, the 5' portion of the probe is about 3-10 bases long and the 3' portion of the probe is at least about 25 nucleotides long (such as about 25-200, at least about 25-100, or at least about 25-50 nucleotides long).
  • different gene fusions may contain a common portion (for example distinct gene fusions may include the same or a similar 5' portion, but different 3' portions, or vice versa), and the difference in the point of fusions that varies may only vary by a few bases (for example, 20 or less, such as 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 base).
  • the fusion probe is designed in order to discriminate the fusions, for example by slightly offsetting the probe such that the bases which are different between fusions are internal to the sequence that is captured or hybridizes to the programming linker, such that the either the mismatched probe or the mismatched target bases will be hydrolyzed by the nuclease, and then the short matched region left will melt and be hydrolyzed, thus preventing the mismatched probe from being captured.
  • programming linkers can be utilized to distinguish the gene fusions (for example, based on spatial location on an array).
  • the probe can be designed to have only a few bases covering the sequence that differs between fusions, with the label located at that end such that it is protected when the sequence is hybridized, and otherwise hydrolyzed and thus not detected, and it is captured by the common gene sequence, such that all probes are captured, but only the correctly matched probes produce a detectable signal.
  • Exemplary fusion probes include those shown in Table 2. Other exemplary fusion probes are shown in Tables 4, 7, and 8 (below). One of skill in the art can design fusion probes for any gene fusion where the fusion point of the two genes is known, for example those provided in Table 1, above.
  • gagccccttgcagTCCTGGTACCT 58 14 agccccttgcagTCCTGGTACCTG 59.1 15 gccccttgcagTCCTGGTACCTGG 59.9 16 ccccttgcagTCCTGGTACCTGGG 59.6 17 gcgagccccttgcagCCTAACGGC 62.7 18 cgagccccttgcagCCTAACGGCA 61.9 19 gagcccttgcagCCTAACGGCAG
  • the probe is a "flanking" probe, which hybridizes to a portion of the full-length gene, a portion of which is included in the gene fusion.
  • the flanking probes are complementary to sequence present in the wild type gene and may also be complementary to sequence present in the gene fusion. This is presented schematically in FIG. 3.
  • a "5' flanking probe” is a probe that is complementary to a sequence that is 5 Of a fusion point or breakpoint in the wild- type (non-fusion) gene (for example, 5' probe 1 or 5' probe 2 in FIG. 3).
  • a "3' flanking probe” is a probe that is complementary to a sequence that is 3 Of a fusion point or a breakpoint in the wild type (non-fusion) gene (for example, 3' probe 1 or 3' probe 2 in FIG. 3).
  • a fusion probe is about 10-200 nucleotides in length (including but not limited to about 20-100, 25-50, or 30-45 nucleotides in length and others as described above)
  • a fusion probe is at least about 10, 15, 20, 25, 30, 25, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 14, 150, 160, 170, 180, 190, 200, or more nucleotides in length.
  • a fusion between two genes is known to occur and the fusion point is also known.
  • Flanking probes can be designed to be complementary to the 5' gene in the fusion (Gene 1 in FIG. 3) at points 5' and 3' to the known fusion point.
  • flanking probes can be designed to be complementary to the 3' gene in the fusion (Gene 2 in FIG. 3) at points 5' and 3' to the fusion point.
  • flanking probes are provided in Tables 3 and 8.
  • a fusion between two genes is not known to occur, or a fusion is known to occur, but the fusion point is not known.
  • the samples of use in the disclosed methods include any specimen that includes nucleic acid (such as genomic DNA, cDNA, viral DNA or RNA, rRNA, tRNA, mRNA, oligonucleotides, nucleic acid fragments, modified nucleic acids, synthetic nucleic acids, or the like).
  • the sample includes mRNA.
  • the disclosed methods include obtaining the sample prior to analysis of the sample.
  • the disclosed methods include selecting a subject having a tumor, and then in some examples further selecting the target gene fusion to detect based on the subject's tumor (e.g., see Table 1).
  • samples include any conventional environmental or biological samples, including clinical samples obtained from a human or veterinary subject.
  • Exemplary samples include, without limitation, cells, cell lysates, blood smears, cytocentrifuge preparations, cytology smears, bodily fluids (e.g., blood, plasma, serum, saliva, sputum, urine, bronchoalveolar lavage, semen, etc.), tissue biopsies (e.g., tumor biopsies), fine-needle aspirates, and/or tissue sections (e.g., cryostat tissue sections and/or paraffin-embedded tissue sections).
  • the sample includes circulating tumor cells or circulating fetal cells in maternal blood.
  • samples are used directly (e.g., fresh or frozen), or can be manipulated prior to use, for example, by fixation (e.g., using formalin) and/or embedding in wax (such as formalin-fixed paraffin-embedded (FFPE) tissue samples).
  • fixation e.g., using formalin
  • wax such as formalin-fixed paraffin-embedded (FFPE) tissue samples.
  • a sample includes a specimen including bacterial or viral nucleic acids, for example a sample from a subject infected with a virus or bacterium.
  • a sample may also include environmental specimens, for example, water, air, soil, dust, wood, or food or other materials that may contain or be contaminated with a pathogen.
  • a sample from a subject is known in the art. For example, methods of obtaining tissue or cell samples are routine. Exemplary samples may be obtained from normal cells or tissues, or from neoplastic cells or tissues. Neoplasia is a biological condition in which one or more cells have undergone characteristic anaplasia with loss of differentiation, increased rate of growth, invasion of surrounding tissue, and which cells may be capable of metastasis.
  • a biological sample includes a tumor sample, such as a sample containing neoplastic cells.
  • Exemplary neoplastic cells or tissues may be included in or isolated from solid tumors, including lung cancer (e.g., non-small cell lung cancer, such as lung squamous cell carcinoma), breast carcinomas (e.g. lobular and duct carcinomas), adrenocortical cancer, ameloblastoma, ampullary cancer, bladder cancer, bone cancer, cervical cancer, cholangioma, colorectal cancer, endometrial cancer, esophageal cancer, gastric cancer, glioma, granular call tumor, head and neck cancer, hepatocellular cancer, hydatiform mole, lymphoma, melanoma,
  • lung cancer e.g., non-small cell lung cancer, such as lung squamous cell carcinoma
  • breast carcinomas e.g. lobular and duct carcinomas
  • adrenocortical cancer e.g., adrenocortical cancer
  • mesothelioma mesothelioma, myeloma, neuroblastoma, oral cancer, osteochondroma,
  • osteosarcoma ovarian cancer, pancreatic cancer, pilomatricoma, prostate cancer, renal cell cancer, salivary gland tumor, soft tissue tumors, Spitz nevus, squamous cell cancer, teratoid cancer, and thyroid cancer.
  • Exemplary neoplastic cells may also be included in or isolated from hematological cancers including leukemias, including acute leukemias (such as acute lymphocytic leukemia, acute myelocytic leukemia, acute myelogenous leukemia and myeloblasts, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (such as chronic myelocytic (granulocytic) leukemia, chronic myelogenous leukemia, and chronic lymphocytic leukemia), polycythemia vera, lymphoma, Hodgkin' s disease, non-Hodgkin' s lymphoma (indolent and high grade forms), multiple myeloma, Waldenstrom' s macro globulinemia, heavy chain disease, myelodysplasia syndrome, and myelodysplasia.
  • acute leukemias such as acute lymphocytic le
  • a sample from a tumor that contains cellular material can be obtained by surgical excision of all or part of the tumor, by collecting a fine needle aspirate from the tumor, as well as other methods known in the art.
  • a tissue or cell sample is applied to a substrate and analyzed to determine presence of a gene fusion.
  • a solid support useful in a disclosed method need only bear the biological sample and, optionally, but advantageously, permit the convenient detection of components (e.g., proteins and/or nucleic acid sequences) in the sample.
  • Exemplary supports include microscope slides (e.g., glass microscope slides or plastic microscope slides), coverslips (e.g., glass coverslips or plastic coverslips), tissue culture dishes, multi-well plates, membranes (e.g., nitrocellulose or polyvinylidene fluoride (PVDF)) or BIACORE chips.
  • microscope slides e.g., glass microscope slides or plastic microscope slides
  • coverslips e.g., glass coverslips or plastic coverslips
  • tissue culture dishes e.g., multi-well plates
  • membranes e.g., nitrocellulose or polyvinylidene fluoride (PVDF)
  • BIACORE chips e.g., BIACORE chips.
  • cells in the sample are lysed or permeabilized in an aqueous solution (for example using a lysis buffer).
  • the aqueous solution or lysis buffer includes detergent (such as sodium dodecyl sulfate) and one or more chaotropic agents (such as formamide, guanidinium HC1, guanidinium isothiocyanate, or urea).
  • the solution may also contain a buffer (for example SSC).
  • the lysis buffer includes about 15% to 25% formamide (v/v) about 0.01% to 0.1% SDS, and about 0.5-6X SSC (for example, about 3X SSC).
  • the buffer may optionally include tRNA (for example, about 0.001 to about 2.0 mg/ml) or a ribonuclease.
  • the lysis buffer may also include a pH indicator, such as Phenol Red.
  • the lysis buffer includes 20% formamide, 3X SSC (79.5%), 0.05% SDS, 1 ⁇ g/ml tRNA, and 1 mg/ml Phenol Red.
  • Cells are incubated in the aqueous solution for a sufficient period of time (such as about 1 minute to about 60 minutes, for example about 5 minutes to about 20 minutes, or about 10 minutes) and at a sufficient temperature (such as about 22°C to about 115°C, for example, about 37 °C to about 105°C, or about 90°C to about 100°C) to lyse or permeabilize the cell.
  • lysis is performed at about 95°C, if the gene fusion nucleic acid to be detected is RNA.
  • lysis is performed at about 105°C, if the gene fusion nucleic acid to be detected is DNA.
  • lysis conditions can be such that genomic DNA is not accessible to the probes whereas RNA (for example, mRNA) is, or such that the RNA is destroyed and only the DNA is accessible for probe hybridization.
  • the lysis step includes incubating the sample at about 95°C for about 5- 15 minutes to denature the RNA in the sample, but not the genomic DNA.
  • the lysis step includes incubating the sample at about 105°C for about 5- 15 minutes to denature both the RNA and the genomic DNA in the sample.
  • the crude cell lysate is used directly without further purification. The cells may be lysed in the presence or absence of one or more of the disclosed probes.
  • the one or more probes can be subsequently added to the crude lysate.
  • nucleic acids such as DNA and/or RNA
  • tissue samples are prepared by fixing and embedding the tissue in a medium or include a cell suspension is prepared as a monolayer on a solid support (such as a glass slide), for example by smearing or centrifuging cells onto the solid support.
  • a solid support such as a glass slide
  • fresh frozen (for example, unfixed) tissue or tissue sections may be used in the methods disclosed herein. The tissue sections are used in the methods disclosed herein, for example by placing all or a portion of the section in the lysis buffer and proceeding as described for other sample types.
  • an embedding medium is used.
  • An embedding medium is an inert material in which tissues and/or cells are embedded to help preserve them for future analysis. Embedding also enables tissue samples to be sliced into thin sections. Embedding media include paraffin, celloidin, OCTTM compound, agar, plastics, or acrylics. Many embedding media are hydrophobic; therefore, the inert material may need to be removed prior to histological or cytological analysis, which utilizes primarily hydrophilic reagents.
  • deparaffinization or dewaxing is broadly used herein to refer to the partial or complete removal of any type of embedding medium from a biological sample.
  • paraffin-embedded tissue sections are dewaxed by passage through organic solvents, such as toluene, xylene, limonene, or other suitable solvents.
  • organic solvents such as toluene, xylene, limonene, or other suitable solvents.
  • a formalin-fixed paraffin embedded sample is not dewaxed prior to cell lysis.
  • Tissues can be fixed by any suitable process, including perfusion or by submersion in a fixative.
  • Fixatives can be classified as cross-linking agents (such as aldehydes, e.g., formaldehyde, paraformaldehyde, and glutaraldehyde, as well as non-aldehyde cross-linking agents), oxidizing agents (e.g., metallic ions and complexes, such as osmium tetroxide and chromic acid), protein-denaturing agents (e.g., acetic acid, methanol, and ethanol), fixatives of unknown mechanism (e.g., mercuric chloride, acetone, and picric acid), combination reagents (e.g., Carnoy's fixative, methacarn, Bouin's fluid, B5 fixative, Rossman's fluid, and Gendre's fluid), microwaves, and miscellaneous fixatives (e.g., excluded volume fixation
  • fixative in preparing samples for IHC is formaldehyde, generally in the form of a formalin solution (4% formaldehyde in a buffer solution, referred to as 10% buffered formalin).
  • the fixative is 10% neutral buffered formalin.
  • This example describes fusion probes for detection of Bcr-Abl fusions and their use in detecting Bcr-Abl fusion nucleic acids.
  • Fusion probes spanning Bcr-Abl fusions were designed and are provided in Table 4.
  • IVT In vitro transcribed
  • mRNA for Bcr-Abl fusion targets was prepared (Table 5). Specific IVT target was added and the signal from an array containing the entire target fusion probes was measured in a checkerboard assay (FIG. 4). IVT target diluted with lysis buffer was incubated with fusion probes at 95 °C for 10-15 minutes, and incubated at 60°C for 6-16 hours to allow for RNA-probe
  • the mixture was treated with SI nuclease (1:40 dilution in SI nuclease buffer) at 50°C for 60-90 minutes to digest unhybridized RNA and probes.
  • the nuclease reaction was stopped (1.6 N NaOH, 0.135 M EDTA pH 8.0) forl5-20 minutes at 95°C and then the mixture was added to a plate including programming linkers specific for the fusion probes (Table 6) and incubated at 50°C for 16-24 hours. Detection linkers (Table 6) were then added and incubated at 60°C for 60-90 minutes. Detection probe was added and incubated at 50°C for 60-90 minutes, then detection solution was added and incubated at 37°C for 60 minutes. Luminescent solution was added and the plate was imaged to detect fusion probe binding to the plate.
  • the probes were generally specific for the intended target (FIG. 4).
  • the probes can be re-designed to eliminate this cross- reactivity, which is believed to arise because the specific fusions are very close to one another, with overlapping bases incorporated into the probe sequences.
  • Target Fusion Bcr sequence (nucleotide Abl sequence (nucleotide positions in NM_021574.2) positions in NM_007313.2)
  • This example describes exemplary methods for detecting a Bcr-Abl fusion gene in a sample utilizing a directly labeled fusion probe.
  • methods that deviate from these specific methods can also be used to successfully detect the presence of a Bcr-Abl gene fusion in a sample.
  • a fusion probe is synthesized which spans the Bcr-Abl E1/A2 fusion site, including four nucleotides of Bcr sequence and 40 nucleotides of Abl sequence (Table 7).
  • the probe is labeled with biotin at the 5' end or about one to two nucleotides from the 5' end.
  • a cell sample is lysed with lysis buffer (for example as described above) and the probe (167 pM) is hybridized to the lysed sample.
  • the sample is treated with SI nuclease to remove non-hybridized nucleic acids as described above.
  • SI nuclease treatment also removes the non-hybridized portion of the fusion probe hybridized to the wild- type Abl nucleic acid, including the biotin label (for example, see FIG. 2).
  • the remaining fusion probe, which is hybridized to Bcr-Abl fusion nucleic acid is detected utilizing avidin-horseradish peroxidase or avidin-phycoerythrin. Detection of signal indicates the presence of a Bcr-Abl gene fusion in the sample.
  • This example describes detection of EML4-ALK fusion variants with fusion probes.
  • SI nuclease diluted 1:40 in SI nuclease buffer (0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.225 M ZnS0 4 , 0.05% KATHON) was added to the sample.
  • the sample was incubated at 50°C for 60-90 minutes to digest unbound nucleic acids.
  • An ARRAYPLATE (HTG Molecular) including programming linkers including a portion complementary to a portion of the fusion probe at spatially distinct locations was prepared by diluting 20X wash solution (20X SSC, 0.95% TWEEN-20, 0.05% KATHON) heated to 50°C by 1:20, adding 250 ⁇ per well to the ARRAYPLATE, incubating for 10-50 seconds and emptying the wells. This was repeated for six cycles. After the last wash, 40 ⁇ of programming solution including 5 nM of each programming linker was added per well and the plate was incubated at 60°C for 60-90 minutes and then washed.
  • 20X wash solution (20X SSC, 0.95% TWEEN-20, 0.05% KATHON) heated to 50°C by 1:20, adding 250 ⁇ per well to the ARRAYPLATE, incubating for 10-50 seconds and emptying the wells. This was repeated for six cycles. After the last wash, 40 ⁇ of programming solution including 5 nM of each programming linker was added per well and
  • a Stop plate was prepared with 10 ⁇ SI stop solution (1.6 N NaOH, 0.135 M EDTA, pH 8.0) and the entire sample was transferred to the stop plate following nuclease incubation.
  • the stop plate was incubated at 95°C for 15-20 minutes to inactivate the SI nuclease and hydrolyze bound RNA.
  • the plate was allowed to cool at room temperature for 5-10 minutes and 10 ⁇ neutralization solution (1 M HEPES, pH 7.5, 6X SSC, 1.6 N HCl) was added to the lower aqueous phase of the Stop Plate and mixed.
  • the wash solution was removed from the ARRAYPLATE and 60 ⁇ of the lower aqueous phase was transferred from the Stop plate to the ARRAYPLATE.
  • the remaining 70 ⁇ of the upper oil phase of the Stop plate was transferred to the ARRAYPLATE and the plate was incubated at 50°C for 16-24 hours to allow probe hybridization to the plate.
  • the ARRAYPLATE was then washed with wash solution and 40 ⁇ of detection linker solution (5 nM) was added and incubated for 60-90 minutes at 60°C to allow detection linker hybridization.
  • 40 ⁇ of detection probe (5 nM) was added to the plate and incubated for 60-90 minutes at 50°C.
  • 40 ⁇ of detection enzyme solution was added to the plate and incubated at 37 °C for 60 minutes. The plate was washed and incubated at room temperature with shaking for 15-30 minutes.
  • FIG. 6A-H Titration curves with increasing amount of IVT fusion mRNA were performed with each EML4-ALK probe. The results for each probe are shown in FIG. 6A-H. All probes provided sensitive detection of IVT mRNA.
  • the observed differences in signal intensities may be due to differences in efficiency of hybridization of the probes to their target fusion sequence, the quality of the IVTs, or other factors.
  • This example describes design and testing of 5' and 3' flanking ALK probes.
  • IVT mRNAs Two IVT mRNAs were utilized in these experiments. One was a full-length ALK IVT generated from a commercially available clone. The second IVT was designed to include only the 16 target sequences (Table 9). Experiments were carried out as described in Example 3. Table 9. ALK 5' and 3' flanking probe target sequences
  • This example describes exemplary methods of detecting the presence of a gene fusion in a sample utilizing probes flanking the fusion region. However, one skilled in the art will appreciate that methods that deviate from these specific methods can also be used to successfully detect the presence of a gene fusion in a sample.
  • a sample such as a tumor sample or a blood sample is collected from a subject having or suspected to have a target gene fusion.
  • Cells in the sample are lysed with lysis buffer (described above) at 60°C for 6-16 hours in the presence of a 5' flanking probe and a 3' flanking probe for one of the genes in the target gene fusion (for example, flanking probes shown in Table 3 or Table 8).
  • the mixture is treated with SI nuclease (1:40 dilution in SI nuclease buffer) at 50°C for 60-90 minutes to digest unhybridized RNA and probes.
  • the nuclease reaction is stopped (1.6 N NaOH, 0.135 M EDTA pH 8.0) forl5-20 minutes at 95°C and then the mixture is added to a plate including programming linkers specific for the flanking probes and incubated at 50°C for 16-24 hours. Detection linkers are then added and incubated at 60°C for 60-90 minutes. Detection probe is added and incubated at 50°C for 60-90 minutes, then detection solution is added and incubated at 37°C for 60 minutes. Luminescent solution is added and the plate is imaged to detect fusion probe binding to the plate.
  • a ratio of the signal intensity of the 5' flanking probe to the 3' flanking probe is calculated. If the ratio is not statistically different from one, then the target gene fusion is not present in the sample. If the flanking probes are complementary to the 5' gene in the target gene fusion, then the gene fusion is present in the sample if the ratio is statistically significantly greater than one. If the flanking probes are complementary to the 3' gene in the target gene fusion, then the gene fusion is present in the sample if the ratio is statistically significantly less than one.
  • This example describes exemplary methods of detecting a gene fusion in a sample that include utilizing a microarray.
  • methods that deviate from these specific methods can also be used to successfully detect the presence of a gene fusion in a sample.
  • Lysis buffer, mineral oil (to prevent evaporation) and 167 pM final concentration of one or more fusion probes and/or flanking probes are added to a sample including cells.
  • the sample is heated at 95°C for 10-15 minutes and then incubated at 60°C for 6-16 hours for RNA-probe hybridization. If the sample is FFPE tissue or cells, the sample is treated with 1 mg/ml proteinase K at 50°C prior to incubation at 60°C.
  • SI nuclease is diluted 1:40 in SI nuclease buffer (0.25 M sodium acetate, pH 4.5, 1.4 M NaCl, 0.225 M ZnS0 4 , 0.05% KATHON) and added to the sample. The sample is incubated at 50°C for 60-90 minutes to digest unbound nucleic acids.
  • An ARRAYPLATE (HTG Molecular) including programming linkers including a portion complementary to a portion of the fusion probe at spatially distinct locations is prepared by diluting 20X wash solution (20X SSC, 0.95% TWEEN-20, 0.05% KATHON) heated to 50°C by 1:20, adding 250 ⁇ per well to the ARRAYPLATE, incubating for 10-50 seconds and emptying the wells. This is repeated for six cycles. After the last wash, 40 ⁇ of programming solution including 5 nM of each programming linker is added per well and the plate is incubated at 60°C for 60-90 minutes and then washed.
  • 20X wash solution (20X SSC, 0.95% TWEEN-20, 0.05% KATHON) heated to 50°C by 1:20, adding 250 ⁇ per well to the ARRAYPLATE, incubating for 10-50 seconds and emptying the wells. This is repeated for six cycles. After the last wash, 40 ⁇ of programming solution including 5 nM of each programming linker is added per well and
  • a Stop plate is prepared with 10 ⁇ SI stop solution (1.6 N NaOH, 0.135 M EDTA, pH 8.0) and the entire sample (120 ⁇ ) is transferred to the stop plate following nuclease incubation.
  • the stop plate is incubated at 95°C for 15-20 minutes to inactivate the SI nuclease and hydrolyze bound RNA.
  • the plate is allowed to cool at room temperature for 5-10 minutes and 10 ⁇ neutralization solution (1 M HEPES, pH 7.5, 6X SSC, 1.6 N HC1) is added to the lower aqueous phase of the Stop Plate and mixed.
  • the wash solution is removed from the ARRAYPLATE and 60 ⁇ of the lower aqueous phase is transferred from the Stop plate to the ARRAYPLATE.
  • the remaining 70 ⁇ of the upper oil phase of the Stop plate is transferred to the
  • ARRAYPLATE and the plate is incubated at 50°C for 16-24 hours to allow probe hybridization to the plate.
  • the ARRAYPLATE is then wash with wash solution and 40 ⁇ of detection linker solution (5 nM) is added and incubated for 60-90 minutes at 60°C to allow detection linker hybridization.
  • 40 ⁇ of detection probe (5 nM) is added to the plate and incubated for 60-90 minutes at 50°C.
  • SUPERCAPELLA imager Signal intensity indicates presence and amount of fusion probe hybridization, indicating presence of the target gene fusion (if a fusion probe is used), or presence of full length and/or gene (if flanking probes are used).

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Abstract

La présente invention concerne des procédés de détection de la présence d'une fusion de gènes dans un échantillon provenant d'un sujet. Dans certains modes de réalisation, l'invention concerne les procédés de détection de la présence d'un gène de fusion dans un échantillon provenant d'un sujet qui utilisent une sonde de fusion qui étend le point de fusion entre deux acides nucléiques ou gènes, et de détection de la sonde de fusion après un traitement par une nucléase. Dans d'autres modes de réalisation, l'invention concerne les procédés de détection de la présence d'un gène de fusion dans un échantillon provenant d'un sujet qui utilisent au moins deux sondes qui flanquent le point de fusion entre deux acides nucléiques ou gènes, et de détection de ces sondes après un traitement par une nucléase. Dans des modes de réalisation supplémentaires, les procédés peuvent comprendre la détermination du pourcentage de fusion de gènes dans l'échantillon par rapport au premier acide nucléique ou au second acide nucléique.
EP11868918.1A 2011-07-01 2011-12-07 Procédés de détection de fusions de gènes Active EP2726628B1 (fr)

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